rnaseq
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nf-core
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Following up on a thread on Slack in #modules, discussing with @drpatelh and @grst: - integration of Rmarkdown with Nextflow - adding Rmarkdown at the end of nf-core pipelines, to...
See https://github.com/nf-core/rnaseq/pull/264 I think this is something maybe we can revisit when we convert this pipeline to DSL2 @heuermh ? Will close the open PR for now in favour of...
Especially with low-input non-human samples, a useful QC step would be to screen for unexpected species (e.g. human, ecoli) - https://github.com/csawye01/nf-core-demultiplex/blob/d336df6dc08caed44505e286f9a47e386986d50c/main.nf#L53 - https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
This PR fixes #722 by adding small clarifications on `salmon` output files. ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ]...
I was wondering how to filter out multimapping reads when running the pipeline with the aligner option: star_rsem. I tried several things (modify STAR command and run it offline) and...
The operator chain `.collect().ifEmpty{[]}` could be replaced with `toList()` simplifying a bit the code https://github.com/nf-core/rnaseq/blob/e049f51f0214b2aef7624b9dd496a404a7c34d14/workflows/rnaseq.nf#L768
### Description of the bug I have been testing the execution of the pipeline on an HPC. Despite performing the execution with 32 threads, the time (for 1 fastq pair-end...
### Description of the bug A fasta header can contain comments together with the name of the contig. Example: `>HLA-DRB1*16:02:01 HLA00878` The corresponding line in the decoy.txt file to be...
